We have studied the genetic defect that leads to deficiency of apoC-II in e patients with apoC-II deficiency from independent kindreds. The first patient from Hamburg, West Germany, was found to have a single base substitution (guanosine for a cytosine,) at the first base of the donor splice site of intron II of the apoC-II gene by sequence analysis. This mutation should abolish normal splicing at this site and ultimately lead to the deficiency of plasma apoC- II observed in this kindred. Analysis of total RNA isolated from the patients liver by Northern, slot blot, and in situ RNA hybridization, as well as evaluation of the intrahepatic apoC-II content by immunohistochemistry confirmed the results of our sequence analysis. The second patient from Nijmegen, the Netherlands was found to have a deletion of a cytosine at position # 2943 of exon 3 of the apoC- II gene. This mutation results in the formation of a premature termination codon at a position corresponding to amino acid #18 of normal apoC-II. As a result, this mutation leads to the formation of a truncated apoC-II that is unlikely to activate lipoprotein lipase and thus, leads to apoC-II deficiency in this kindred. Total RNA isolated from the liver of a third patient with apoC-II deficiency was analyzed by Northern, slot blot and in situ RNA hybridization which revealed approximately normal levels of a normal sized apoC-II message. Immunohistochemical analysis showed normal to increased amounts of intrahepatic C-II apolipoprotein. We postulate that the defect in this patient from Padova with normal intrahepatic apoC-II mRNA and protein, but deficiency of apoC-II in plasma is a mutation in the coding portion of the apoC- II gene that results in abnormal secretion or enhanced catabolism of apoC-II.